A longitudinal experiment demonstrates that honey bee colonies managed organically are as healthy and productive as those managed conventionally.

Honey bee colony management is critical to mitigating the negative effects of biotic and abiotic stressors. However, there is significant variation in the practices implemented by beekeepers, which results in varying management systems. This longitudinal study incorporated a systems approach to experimentally test the role of three representative beekeeping management systems (conventional, organic, and chemical-free) on the health and productivity of stationary honey-producing colonies over 3 years. We found that the survival rates for colonies in the conventional and organic management systems were equivalent, but around 2.8 times greater than the survival under chemical-free management. Honey production was also similar, with 102% and 119% more honey produced in conventional and organic management systems, respectively, than in the chemical-free management system. We also report significant differences in biomarkers of health including pathogen levels (DWV, IAPV, Vairimorpha apis, Vairimorpha ceranae) and gene expression (def-1, hym, nkd, vg). Our results experimentally demonstrate that beekeeping management practices are key drivers of survival and productivity of managed honey bee colonies. More importantly, we found that the organic management system-which uses organic-approved chemicals for mite control-supports healthy and productive colonies, and can be incorporated as a sustainable approach for stationary honey-producing beekeeping operations.

Six years of wild bee monitoring shows changes in biodiversity within and across years and declines in abundance.

Wild bees form diverse communities that pollinate plants in both native and agricultural ecosystems making them both ecologically and economically important. The growing evidence of bee declines has sparked increased interest in monitoring bee community and population dynamics using standardized methods. Here, we studied the dynamics of bee biodiversity within and across years by monitoring wild bees adjacent to four apple orchard locations in Southern Pennsylvania, USA. We collected bees using passive Blue Vane traps continuously from April to October for 6 years (2014-2019) amassing over 26,000 bees representing 144 species. We quantified total abundance, richness, diversity, composition, and phylogenetic structure. There were large seasonal changes in all measures of biodiversity with month explaining an average of 72% of the variation in our models. Changes over time were less dramatic with years explaining an average of 44% of the variation in biodiversity metrics. We found declines in all measures of biodiversity especially in the last 3 years, though additional years of sampling are needed to say if changes over time are part of a larger trend. Analyses of population dynamics over time for the 40 most abundant species indicate that about one third of species showed at least some evidence for declines in abundance. Bee family explained variation in species-level seasonal patterns but we found no consistent family-level patterns in declines, though bumble bees and sweat bees were groups that declined the most. Overall, our results show that season-wide standardized sampling across multiple years can reveal nuanced patterns in bee biodiversity, phenological patterns of bees, and population trends over time of many co-occurring species. These datasets could be used to quantify the relative effects that different aspects of environmental change have on bee communities and to help identify species of conservation concern.

Large ecosystem-scale effects of restoration fail to mitigate impacts of land-use legacies in longleaf pine savannas.

Ecological restoration is a global priority, with potential to reverse biodiversity declines and promote ecosystem functioning. Yet, successful restoration is challenged by lingering legacies of past land-use activities, which are pervasive on lands available for restoration. Although legacies can persist for centuries following cessation of human land uses such as agriculture, we currently lack understanding of how land-use legacies affect entire ecosystems, how they influence restoration outcomes, or whether restoration can mitigate legacy effects. Using a large-scale experiment, we evaluated how restoration by tree thinning and land-use legacies from prior cultivation and subsequent conversion to pine plantations affect fire-suppressed longleaf pine savannas. We evaluated 45 ecological properties across four categories: 1) abiotic attributes, 2) organism abundances, 3) species diversity, and 4) species interactions. The effects of restoration and land-use legacies were pervasive, shaping all categories of properties, with restoration effects roughly twice the magnitude of legacy effects. Restoration effects were of comparable magnitude in savannas with and without a history of intensive human land use; however, restoration did not mitigate numerous legacy effects present prior to restoration. As a result, savannas with a history of intensive human land use supported altered properties, especially related to soils, even after restoration. The signature of past human land-use activities can be remarkably persistent in the face of intensive restoration, influencing the outcome of restoration across diverse ecological properties. Understanding and mitigating land-use legacies will maximize the potential to restore degraded ecosystems.

Agricultural land-use history does not reduce woodland understory herb establishment.

Agricultural land use is a leading cause of habitat degradation, leaving a legacy of ecological impacts long after agriculture has ceased. Yet the mechanisms for legacy effects, such as altered plant community composition, are not well understood. In particular, whether plant community recovery is limited by an inability of populations to establish within post-agricultural areas, owing to altered environmental conditions within these areas, remains poorly known. We evaluated this hypothesis of post-agricultural establishment limitation through a field experiment within longleaf pine woodlands in South Carolina (USA) and a greenhouse experiment using field-collected soils from these sites. In the field, we sowed seeds of 12 understory plant species associated with remnants (no known history of agriculture) into 27 paired remnant and post-agricultural woodlands. We found that post-agricultural woodlands supported higher establishment, resulting in greater species richness of sown species. These results were context dependent, however, with higher establishment in post-agricultural woodlands only when sites were frequently burned, had less leaf litter, or had less sandy soils. In the greenhouse, we found that agricultural history had no impact on plant growth or survival, suggesting that establishment limitation is unlikely driven by differences in soils associated with agricultural history when environmental conditions are not stressful. Rather, the potential for establishment in post-agricultural habitats can be higher than in remnant habitats, with the strength of this effect determined by fire frequency and soil characteristics.

The ecological importance of intraspecific variation.

Human activity is causing wild populations to experience rapid trait change and local extirpation. The resulting effects on intraspecific variation could have substantial consequences for ecological processes and ecosystem services. Although researchers have long acknowledged that variation among species influences the surrounding environment, only recently has evidence accumulated for the ecological importance of variation within species. We conducted a meta-analysis comparing the ecological effects of variation within a species (intraspecific effects) with the effects of replacement or removal of that species (species effects). We evaluated direct and indirect ecological responses, including changes in abundance (or biomass), rates of ecological processes and changes in community composition. Our results show that intraspecific effects are often comparable to, and sometimes stronger than, species effects. Species effects tend to be larger for direct ecological responses (for example, through consumption), whereas intraspecific effects and species effects tend to be similar for indirect responses (for example, through trophic cascades). Intraspecific effects are especially strong when indirect interactions alter community composition. Our results summarize data from the first generation of studies examining the relative ecological effects of intraspecific variation. Our conclusions can help inform the design of future experiments and the formulation of strategies to quantify and conserve biodiversity.

Agricultural land-use history causes persistent loss of plant phylogenetic diversity.

Intensive land use activities, such as agriculture, are a leading cause of biodiversity loss and can have lasting impacts on ecological systems. Yet, few studies have investigated how land-use legacies impact phylogenetic diversity (the total amount of evolutionary history in a community) or how restoration activities might mitigate legacy effects on biodiversity. We studied ground-layer plant communities in 27 pairs of Remnant (no agricultural history) and Post-agricultural (agriculture abandoned >60 yr ago) longleaf pine savannas, half of which we restored by thinning trees to reinstate open savanna conditions. We found that agricultural history had no impact on species richness, but did alter community composition and reduce phylogenetic diversity by 566 million years/1,000 m2 . This loss of phylogenetic diversity in post-agricultural savannas was due to, in part, a reduction in the average evolutionary distance between pairs of closely related species, that is, increased phylogenetic clustering. Habitat restoration increased species richness by 27% and phylogenetic diversity by 914 million years but did not eliminate the effects of agricultural land use on community composition and phylogenetic structure. These results demonstrate the persistence of agricultural legacies, even in the face of intensive restoration efforts, and the importance of considering biodiversity broadly when evaluating human impacts on ecosystems.

Plant domestication slows pest evolution.

Agricultural practices such as breeding resistant varieties and pesticide use can cause rapid evolution of pest species, but it remains unknown how plant domestication itself impacts pest contemporary evolution. Using experimental evolution on a comparative phylogenetic scale, we compared the evolutionary dynamics of a globally important economic pest - the green peach aphid (Myzus persicae) - growing on 34 plant taxa, represented by 17 crop species and their wild relatives. Domestication slowed aphid evolution by 13.5%, maintained 10.4% greater aphid genotypic diversity and 5.6% higher genotypic richness. The direction of evolution (i.e. which genotypes increased in frequency) differed among independent domestication events but was correlated with specific plant traits. Individual-based simulation models suggested that domestication affects aphid evolution directly by reducing the strength of selection and indirectly by increasing aphid density and thus weakening genetic drift. Our results suggest that phenotypic changes during domestication can alter pest evolutionary dynamics.

Ecological effects of aphid abundance, genotypic variation, and contemporary evolution on plants.

Genetic variation and contemporary evolution within populations can shape the strength and nature of species interactions, but the relative importance of these forces compared to other ecological factors is unclear. We conducted a field experiment testing the effects of genotypic variation, abundance, and presence/absence of green peach aphids (Myzus persicae) on the growth, leaf nitrogen, and carbon of two plant species (Brassica napus and Solanum nigrum). Aphid genotype affected B. napus but not S. nigrum biomass explaining 20 and 7% of the total variation, respectively. Averaging across both plant species, the presence/absence of aphids had a 1.6× larger effect size (Cohen's d) than aphid genotype, and aphid abundance had the strongest negative effects on plant biomass explaining 29% of the total variation. On B. napus, aphid genotypes had different effects on leaf nitrogen depending on their abundance. Aphids did not influence leaf nitrogen in S. nigrum nor leaf carbon in either species. We conducted a second experiment in the field to test whether contemporary evolution could affect plant performance. Aphid populations evolved in as little as five generations, but the rate and direction of this evolution did not consistently vary between plant species. On one host species (B. napus), faster evolving populations had greater negative effects on host plant biomass, with aphid evolutionary rate explaining 23% of the variation in host plant biomass. Together, these results show that genetic variation and evolution in an insect herbivore can play important roles in shaping host plant ecology.

The impact of domestication on resistance to two generalist herbivores across 29 independent domestication events.

The domestication of crops is among the most important innovations in human history. Here, we test the hypothesis that cultivation and artificial selection for increased productivity of crops reduced plant defenses against herbivores. We compared the performance of two economically important generalist herbivores - the leaf-chewing beet armyworm (Spodoptera exigua) and the phloem-feeding green peach aphid (Myzus persicae) - across 29 crop species and their closely related wild relatives. We also measured putative morphological and chemical defensive traits and correlated them with herbivore performance. We show that, on average, domestication significantly reduced resistance to S. exigua, but not M. persicae, and that most independent domestication events did not cause differences in resistance to either herbivore. In addition, we found that multiple plant traits predicted resistance to S. exigua and M. persicae, and that domestication frequently altered the strength and direction of correlations between these traits and herbivore performance. Our results show that domestication can alter plant defenses, but does not cause strong allocation tradeoffs as predicted by plant defense theory. These results have important implications for understanding the evolutionary ecology of species interactions and for the search for potential resistance traits to be targeted in crop breeding.

Contemporary evolution of plant growth rate following experimental removal of herbivores.

Herbivores are credited with driving the evolutionary diversification of plant defensive strategies over macroevolutionary time. For this to be true, herbivores must also cause short-term evolution within plant populations, but few studies have experimentally tested this prediction. We addressed this gap using a long-term manipulative field experiment where exclosures protected 22 plant populations from natural rabbit herbivory for <1 to 26 years. We collected seeds of Rumex acetosa L. (Polygonaceae) from our plots and grew them in a common greenhouse environment to quantify evolved differences among populations in individual plant growth rate, tolerance to herbivory, competitive ability, and the concentration of secondary metabolites (tannins and oxalate) implicated in defense against herbivores. In 26 years without rabbit herbivory, plant growth rate decreased linearly by 30%. We argue that plant growth rate has evolved as a defense against intense rabbit herbivory. In contrast, we found no change in tolerance to herbivory or concentrations of secondary metabolites. We also found no change in competitive ability, suggesting that contemporary evolution may not feed back to alter ecological interactions within this plant community. Our results combined with those of other studies show that the evolution of gross morphological traits such as growth rate in response to herbivory may be common, which calls into question assumptions about some of the most popular theories of plant defense.

Habitat patch shape, not corridors, determines herbivory and fruit production of an annual plant.

Habitat corridors confer many conservation benefits by increasing movement of organisms between habitat patches, but the benefits for some species may exact costs for others. For example, corridors may increase the abundance of consumers in a habitat to the detriment of the species they consume. In this study we assessed the impact of corridors on insect herbivory of a native plant, Solanum americanum, in large-scale, experimentally fragmented landscapes. We quantified leaf herbivory and assessed fruit production as a proxy for plant fitness. We also conducted field surveys of grasshoppers (Orthoptera), a group of abundant, generalist herbivores that feed on S. americanum, and we used exclosure cages to explicitly link grasshopper herbivory to fruit production of individual S. americanum. The presence of corridors did not increase herbivory or decrease plant fruit production. Likewise, corridors did not increase grasshopper abundance. Instead, patches in our landscapes with the least amount of edge habitat and the greatest amount of warmer "core" area had the highest levels of herbivory, the largest cost to plant fruit production as a result of herbivory, and the most grasshoppers. Thus habitat quality, governed by patch shape, can be more important than connectivity for determining levels of herbivory and the impact of herbivory on plant fitness in fragmented landscapes.

Community genetics: what have we accomplished and where should we be going?

Research in community genetics seeks to understand how the dynamic interplay between ecology and evolution shapes simple and complex communities and ecosystems. A community genetics perspective, however, may not be necessary or informative for all studies and systems. To better understand when and how intraspecific genetic variation and microevolution are important in community and ecosystem ecology, we suggest future research should focus on three areas: (i) determining the relative importance of intraspecific genetic variation compared with other ecological factors in mediating community and ecosystem properties; (ii) understanding the importance of microevolution in shaping ecological dynamics in multi-trophic communities; and (iii) deciphering the phenotypic and associated genetic mechanisms that drive community and ecosystem processes. Here, we identify key areas of research that will increase our understanding of the ecology and evolution of complex communities but that are currently missing in community genetics. We then suggest experiments designed to meet these current gaps.